Digital twins in gastroenterology: From computational modeling to precision medicine and clinical translation

Figure 2 Microbiome digital twin workflow using microbial community-scale metabolic modelling. Stool samples undergo microbial sequencing (16S rRNA or shotgun metagenomics) to determine taxonomic abundances. These data are integrated with dietary constraints and genome-scale metabolic models from the AGORA database to build patient-specific community models using microbial community-scale metabolic modelling. Cooperative tradeoff flux balance analysis is applied to predict steady-state microbial growth and metabolic outputs, including short-chain fatty acid production. ctFBA: Cooperative tradeoff flux balance analysis; MICOM: Microbial community-scale metabolic modelling.